When you have an inflammatory bowel disease, you might feel like there’s a war going on in your gut. And in some respects, that's true: Within the gastrointestinal system, there lies a balance of good and bad bacteria. When that balance gets tipped, the bad guys can take over, leading to abdominal cramps, diarrhea, and other unpleasant symptoms.

Fallout from this bacteria war may be Crohn's disease, a chronic condition that causes inflammation in the gastrointestinal tract. At this point, experts aren’t sure of the exact cause of Crohn’s, but bacteria appear to be involved. That, in turn, may affect your Crohn’s treatment.

“There is some debate among experts about how much of a role the bacteria that live in our gut play in causing inflammation in Crohn’s disease,” says Karlee Ausk, MD, a gastroenterologist at Swedish Gastroenterology, part of the Swedish Medical Center in Seattle. “We do know that when Crohn’s disease is active, the wall of the colon is a little leaky, so bacteria can get in there."

And while the underlying cause of Crohn’s disease is unknown, research notes that genetics, bacteria, and a faulty immune system are involved. Now, scientists at Case Western Reserve University in Cleveland have found another clue to fit with this puzzling condition: a fungus called Candida tropicalis.

In a study published in September 2016 in the journal mBio, researchers examined fecal samples of people with Crohn’s, their family members, and residents living in the surrounding area. People with Crohn's showed higher amounts of the bacteria Serratiamarcescens and Escherichia coli (E. coli), as well as Candida tropicalis, which interacted together to produce a biofilm — a slimy film of bacteria in the body that can attach itself to the intestines and is thought to spawn inflammation. While these findings shed new light on Crohn’s, there are current processes in place to keep symptoms in check.

To counteract an overgrowth of bacteria and yeast and ease Crohn's symptoms, your doctor may prescribe antibiotics as a treatment.

“By using antibiotics in Crohn’s, the hope is that we can decrease bacteria that have invaded the weakened tissue and change the composition of bacteria in the gut,” says Dr. Ausk.

“When patients come in with mild Crohn’s, we frequently treat them first with antibiotics and see how they do,” Ausk says. If antibiotics don’t work, the next step will likely be other Crohn’s medications, such as steroids or biologics.

How Antibiotics Work in Crohn’s Disease

The goal of antibiotics in Crohn’s disease is similar to the goal of other Crohn’s medications and treatments: to put you in remission and improve symptoms, says Andrew Forest, a clinical pharmacy specialist at the University of Maryland Medical Center in Baltimore.

Antibiotics work to achieve remission in a few different ways. “Antibiotics in Crohn’s can treat the actual course of the disease — the progressive inflammation — as well as complications such as abscesses and wound infections,” says Randall Meisner, MD, a gastroenterologist with Spectrum Health Medical Group in Grand Rapids, Michigan.

Research supports this. “In a study using the antibiotic metronidazole, bacteria were cleared, and patients experienced remission for six months,” Forest says. He adds that the antibiotic ciprofloxacin appears to improve Crohn’s symptoms by removing bacteria, mostly E. coli.

Safely Using Antibiotics in Crohn’s Disease

The amount of time you should take antibiotics for Crohn’s will depend on both your comfort level and your doctor's. “Studies on the use of antibiotics in Crohn’s disease range from durations of six weeks to six months,” Meisner says.

In general, Forest says that the longer Crohn’s is treated with antibiotics, the worse the antibiotic side effects are.

The side effects of metronidazole include nausea, vomiting, loss of appetite, diarrhea, dizziness, a metallic taste, and dark or reddish brown urine. When taken long-term, metronidazole may also cause tingling of the hands and feet. Side effects of ciprofloxacin include headaches, nausea, vomiting, abdominal pain, rash, and restlessness. And both antibiotics can promote bad bacteria and infections such as Clostridium difficile, Meisner adds.

“Overall, the most important thing I can tell people taking antibiotics for Crohn’s disease is to take the medication as prescribed and to be sure to inform their providers of any adverse effects they experience,” Forest says. Also be sure to ask your doctor about potential interactions with other medications you might be taking.

Probiotics: An Option Similar to Antibiotics

As an alternative to antibiotics, probiotics — microorganisms derived from food sources such as cultured milk products like yogurt — are also potential Crohn’s treatments. They work similarly to antibiotics by altering the balance of good and bad bacteria in the gut. Probiotics are relatively safe and carry few side effects, so it probably can't hurt to add yogurt to your daily diet. But a review of the few small studies done on probiotics for Crohn's are inconclusive, according to research published in the Cochrane Database of Systematic Reviews.

“There is some evidence that probiotics may work in inflammatory bowel disease, but at this point, there is more evidence for probiotics in ulcerative colitis than for Crohn’s,” says Ausk. More research is needed before probiotics become a mainstay for Crohn’s treatments.